# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 08:48:44 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-(4-phosphono-1H-1,2,3-triazol-1-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cn1cc(nn1)[P](O)(O)=O)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 UKD  UKD  3-(4-phosphono-1H-1,2,3-triazol-1-yl)-L-alanine  L-peptide  21  15  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_UKD
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 UKD  O3   O  OP    -1  -0.886  -19.2331  -24.5331  -29.2755
 UKD  O4   O  O      0  -0.886  -17.6424  -26.5547  -29.1116
 UKD  P    P  P      0   1.124  -18.9920  -26.0128  -29.5847
 UKD  O1   O  OP    -1  -0.887  -20.1805  -26.9255  -29.2776
 UKD  CE2  C  CR5    0  -0.204  -18.8778  -26.0142  -31.4407
 UKD  NE1  N  N      0  -0.343  -18.5344  -27.0735  -32.2221
 UKD  ND1  N  N      0  -0.134  -18.5732  -26.7381  -33.4711
 UKD  CD2  C  CR15   0  -0.116  -19.1375  -24.9749  -32.3028
 UKD  NG   N  NR5    0  -0.244  -18.9333  -25.4695  -33.5382
 UKD  CB   C  CH2    0  -0.275  -19.1415  -24.8032  -34.8094
 UKD  CA   C  CH1    0  -0.234  -20.6165  -24.7666  -35.2022
 UKD  N    N  NH2    0  -0.809  -21.1402  -26.1152  -35.3006
 UKD  C    C  C      0   0.421  -20.8061  -23.9847  -36.5310
 UKD  O    O  O      0  -0.592  -21.6583  -24.4275  -37.3235
 UKD  H3   H  HCR5   0   0.276  -19.4346  -23.9535  -32.1352
 UKD  H4   H  HCH2   0   0.250  -18.5604  -25.3442  -35.5560
 UKD  H5   H  HCH2   0   0.252  -18.7433  -23.7947  -34.7278
 UKD  H6   H  HCH1   0   0.215  -21.1388  -24.1704  -34.4338
 UKD  H7   H  HNH2   0   0.335  -21.4518  -26.4440  -34.3968
 UKD  H8   H  HNH2   0   0.338  -21.9509  -26.0906  -35.9050
 UKD  OXT  O  OC    -1  -0.601  -20.1130  -22.9587  -36.6674

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 UKD  O    C    deloc     1.231  0.020  1.231
 UKD  C    CA   single    1.525  0.021  1.525
 UKD  N    CA   single    1.458  0.019  1.458
 UKD  CA   CB   single    1.521  0.033  1.521
 UKD  CB   NG   single    1.450  0.020  1.450
 UKD  NG   ND1  aromatic  1.320  0.020  1.320
 UKD  NG   CD2  aromatic  1.346  0.020  1.346
 UKD  ND1  NE1  aromatic  1.294  0.020  1.294
 UKD  CD2  CE2  aromatic  1.375  0.020  1.375
 UKD  NE1  CE2  aromatic  1.360  0.020  1.360
 UKD  CE2  P    single    1.860  0.020  1.860
 UKD  P    O4   deloc     1.529  0.020  1.529
 UKD  P    O3   deloc     1.531  0.020  1.531
 UKD  P    O1   deloc     1.530  0.020  1.530
 UKD  CD2  H3   single    0.930  0.020  1.080
 UKD  CB   H4   single    0.970  0.020  1.090
 UKD  CB   H5   single    0.970  0.020  1.090
 UKD  CA   H6   single    0.970  0.020  1.090
 UKD  N    H7   single    0.890  0.020  1.040
 UKD  N    H8   single    0.890  0.020  1.040
 UKD  C    OXT  deloc     1.246  0.020  1.246

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 UKD  CE2  P    O1   104.34  3.000
 UKD  O1   P    O4   114.34  3.000
 UKD  CE2  P    O4   104.73  3.000
 UKD  O1   P    O3   114.45  3.000
 UKD  O4   P    O3   114.77  3.000
 UKD  CE2  P    O3   102.24  3.000
 UKD  CD2  CE2  NE1  106.03  3.000
 UKD  NE1  CE2  P    126.12  3.000
 UKD  CD2  CE2  P    127.84  3.000
 UKD  ND1  NE1  CE2  110.19  3.000
 UKD  NG   ND1  NE1  107.83  3.000
 UKD  H3   CD2  NG   122.22  3.000
 UKD  H3   CD2  CE2  132.18  3.000
 UKD  NG   CD2  CE2  105.60  3.000
 UKD  CB   NG   CD2  127.86  3.000
 UKD  CD2  NG   ND1  110.35  3.000
 UKD  CB   NG   ND1  121.67  3.000
 UKD  H5   CB   H4   108.45  3.000
 UKD  H5   CB   CA   110.54  3.000
 UKD  H4   CB   CA   110.53  3.000
 UKD  H5   CB   NG   107.93  3.000
 UKD  H4   CB   NG   107.21  3.000
 UKD  CA   CB   NG   112.04  3.000
 UKD  H6   CA   C    105.42  3.000
 UKD  H6   CA   N    112.25  3.000
 UKD  C    CA   N    111.00  2.800
 UKD  H6   CA   CB   106.91  3.000
 UKD  N    CA   CB   110.40  1.500
 UKD  C    CA   CB   110.50  1.500
 UKD  H8   N    H7   107.16  3.000
 UKD  H8   N    CA   107.90  3.000
 UKD  H7   N    CA   110.68  3.000
 UKD  OXT  C    O    127.15  3.000
 UKD  OXT  C    CA   120.80  1.700
 UKD  O    C    CA   120.80  1.700

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 UKD  CONST_01  ND1  NG   CD2  CE2    0.00   0.0  0
 UKD  CONST_02  NG   ND1  NE1  CE2    0.00   0.0  0
 UKD  CONST_03  CD2  NG   ND1  NE1    0.00   0.0  0
 UKD  CONST_04  NG   CD2  CE2  NE1    0.00   0.0  0
 UKD  CONST_05  CD2  CE2  NE1  ND1    0.00   0.0  0
 UKD  CONST_06  NG   CD2  CE2  P    180.00   0.0  0
 UKD  CONST_07  ND1  NE1  CE2  P    180.00   0.0  0
 UKD  CONST_08  CB   NG   CD2  CE2  180.00   0.0  0
 UKD  CONST_09  CB   NG   ND1  NE1  180.00   0.0  0
 UKD  CONST_10  H3   CD2  CE2  NE1  180.00   0.0  0
 UKD  Var_01    CD2  CE2  P    O3    -8.19  30.0  2
 UKD  Var_02    CA   CB   NG   ND1   97.47  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 UKD  chir_01  CA  C  N  CB  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 UKD  plan-1  P    0.020
 UKD  plan-1  CE2  0.020
 UKD  plan-1  NE1  0.020
 UKD  plan-1  ND1  0.020
 UKD  plan-1  CD2  0.020
 UKD  plan-1  NG   0.020
 UKD  plan-1  CB   0.020
 UKD  plan-1  H3   0.020
 UKD  plan-2  CA   0.020
 UKD  plan-2  C    0.020
 UKD  plan-2  O    0.020
 UKD  plan-2  OXT  0.020

